Document and Data Source Questions

How can I extract patent data from ChEMBL?

On the interface:

Select the documents view from the main ChEMBL homepage -

Use the lefthand filter panel to select patents -

Local version of the database:

Selected patent data is available in ChEMBL under SRC_ID 38. Patent data from Binding DB is included under SRC_ID 37.

Details on the selection of patents can be found in this publication.

How do I perform a document similarity search?

More details can be found in this Blog post.

We also have an API endpoint: https://www.ebi.ac.uk/chembl/api/data/document_similarity

What data sources are stored in ChEMBL?

ChEMBL consists of data from a wide variety of data sources including scientific literature and patents, deposited data sets, PubChem BioAssay and BindingDB databases, toxicology data sets and drug/clinical candidate resources. The current list of sources is:

Source	Source ID
Scientific Literature	1
GSK Malaria Screening	2
Novartis Malaria Screening	3
St Jude Malaria Screening	4
Sanger Institute Genomics of Drug Sensitivity in Cancer	5
PDBe Ligands	6
PubChem BioAssays	7
Clinical Candidates	8
Orange Book	9
Guide to Receptors and Channels (DEPRECATED)	10
Open TG-GATEs	11
Manually Added Drugs	12
USP Dictionary of USAN and International Drug Names	13
Drugs for Neglected Diseases Initiative (DNDi)	14
DrugMatrix	15
GSK Published Kinase Inhibitor Set	16
MMV Malaria Box	17
TP-search Transporter Database	18
Harvard Malaria Screening	19
WHO-TDR Malaria Screening	20
Deposited Supplementary Bioactivity Data	21
GSK Tuberculosis Screening	22
Open Source Malaria Screening	23
Millipore Kinase Screening (DEPRECATED - MERGED WITH SRC_ID = 1	24
External Project Compounds	25
Gene Expression Atlas Compounds	26
AstraZeneca Deposited Data	27
FDA Approval Packages	28
GSK Kinetoplastid Screening	29
K4DD Project	30
Curated Drug Metabolism Pathways	31
St Jude Leishmania Screening	32
Gates Library compound collection	33
MMV Pathogen Box	34
HeCaToS Compounds	35
Withdrawn Drugs	36
BindingDB Database	37
Patent Bioactivity Data	38
Curated Drug Pharmacokinetic Data	39
CO-ADD antimicrobial screening data	40
WHO Anatomical Therapeutic Chemical Classification	41
British National Formulary	42
Published Kinase Inhibitor Set 2	43
Kuster lab chemical proteomics drug profiling	48
HESi	49
Winzeler Lab Plasmodium Screening Data	51
SARS-CoV-2 Screening Data 2020-21	52
Prodrug active ingredients	53
Donated Chemical Probes - SGC Frankfurt	54
EUbOPEN Chemogenomic Library	55
Salvensis and LSHTM Schistosomiasis screening data	56
IMI-CARE SARS-CoV-2 Data	57
Fraunhofer HDAC6	59
MMV Malaria HGL	60
International Nonproprietary Names	63
Cardiff Schistosomiasis Dataset 2023	64
Literature data from EUbOPEN Chemogenomic Library	65